{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T05:51:05Z","timestamp":1791265865633,"version":"4.1.0"},"reference-count":81,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T00:00:00Z","timestamp":1764288000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.celrep.2025.116776","type":"journal-article","created":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T01:21:17Z","timestamp":1767057677000},"page":"116776","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Phage induction of Staphylococcus aureus pathogenicity islands promotes the CRISPR-Cas adaptive immune response"],"prefix":"10.1016","volume":"45","author":[{"given":"Dalton V.","family":"Banh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory W.","family":"Goldberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9163-0969","authenticated-orcid":false,"given":"Luciano A.","family":"Marraffini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2025.116776_bib1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s41579-019-0299-x","article-title":"Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants","volume":"18","author":"Makarova","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib2","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1126\/science.1138140","article-title":"CRISPR provides acquired resistance against viruses in prokaryotes","volume":"315","author":"Barrangou","year":"2007","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116776_bib3","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1126\/science.1165771","article-title":"CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA","volume":"322","author":"Marraffini","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116776_bib4","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1099\/mic.0.28048-0","article-title":"Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin","volume":"151","author":"Bolotin","year":"2005","journal-title":"Microbiology"},{"key":"10.1016\/j.celrep.2025.116776_bib5","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1007\/s00239-004-0046-3","article-title":"Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements","volume":"60","author":"Mojica","year":"2005","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.celrep.2025.116776_bib6","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1099\/mic.0.27437-0","article-title":"CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies","volume":"151","author":"Pourcel","year":"2005","journal-title":"Microbiology"},{"key":"10.1016\/j.celrep.2025.116776_bib7","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1126\/science.1159689","article-title":"Small CRISPR RNAs guide antiviral defense in prokaryotes","volume":"321","author":"Brouns","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116776_bib8","doi-asserted-by":"crossref","first-page":"2572","DOI":"10.1261\/rna.1246808","article-title":"Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus","volume":"14","author":"Hale","year":"2008","journal-title":"RNA"},{"key":"10.1016\/j.celrep.2025.116776_bib9","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nature09523","article-title":"The CRISPR\/Cas bacterial immune system cleaves bacteriophage and plasmid DNA","volume":"468","author":"Garneau","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib10","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1016\/j.cell.2009.07.040","article-title":"RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex","volume":"139","author":"Hale","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib11","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nsmb.2019","article-title":"Structural basis for CRISPR RNA-guided DNA recognition by Cascade","volume":"18","author":"Jore","year":"2011","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116776_bib12","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2212722119","article-title":"Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements","volume":"119","author":"Eppley","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2025.116776_bib13","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1038\/s41396-018-0156-3","article-title":"Phage-inducible chromosomal islands are ubiquitous within the bacterial universe","volume":"12","author":"Fillol-Salom","year":"2018","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2025.116776_bib14","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1146\/annurev-virology-031413-085446","article-title":"The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites","volume":"2","author":"Penades","year":"2015","journal-title":"Annu. Rev. Virol."},{"key":"10.1016\/j.celrep.2025.116776_bib15","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1046\/j.1365-2958.1998.00947.x","article-title":"The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus","volume":"29","author":"Lindsay","year":"1998","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib16","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1111\/j.1365-2958.2007.06027.x","article-title":"SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage","volume":"67","author":"Ubeda","year":"2008","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib17","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/nature09065","article-title":"Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands","volume":"465","author":"Tormo-Mas","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib18","doi-asserted-by":"crossref","first-page":"7520","DOI":"10.1128\/JB.00738-07","article-title":"Transducing particles of Staphylococcus aureus pathogenicity island SaPI1 are comprised of helper phage-encoded proteins","volume":"189","author":"Tallent","year":"2007","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.celrep.2025.116776_bib19","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1128\/JB.01349-07","article-title":"Staphylococcus aureus pathogenicity island DNA is packaged in particles composed of phage proteins","volume":"190","author":"Tormo","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.celrep.2025.116776_bib20","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1046\/j.1365-2958.2001.02488.x","article-title":"Molecular genetics of SaPI1--a mobile pathogenicity island in Staphylococcus aureus","volume":"41","author":"Ruzin","year":"2001","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib21","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1111\/j.1365-2958.2010.07312.x","article-title":"Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPI-carried variants of von Willebrand factor-binding protein","volume":"77","author":"Viana","year":"2010","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib22","doi-asserted-by":"crossref","first-page":"3248","DOI":"10.1016\/j.cell.2022.07.014","article-title":"Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors","volume":"185","author":"Fillol-Salom","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib23","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature14299","article-title":"In vivo genome editing using Staphylococcus aureus Cas9","volume":"520","author":"Ran","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib24","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/j.cell.2015.04.027","article-title":"Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity","volume":"161","author":"Samai","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib25","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.molcel.2016.03.024","article-title":"Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition","volume":"62","author":"Kazlauskiene","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib26","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1126\/science.aao0100","article-title":"A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems","volume":"357","author":"Kazlauskiene","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116776_bib27","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nature23467","article-title":"Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers","volume":"548","author":"Niewoehner","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib28","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1016\/j.cell.2015.12.053","article-title":"Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity","volume":"164","author":"Jiang","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib29","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/s41564-018-0353-x","article-title":"Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR-Cas immunity","volume":"4","author":"Rostol","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib30","doi-asserted-by":"crossref","first-page":"11109","DOI":"10.1093\/nar\/gkac855","article-title":"Non-canonical Staphylococcus aureus pathogenicity island repression","volume":"50","author":"Miguel-Romero","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib31","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.jmb.2010.11.047","article-title":"A conformational switch involved in maturation of Staphylococcus aureus bacteriophage 80alpha capsids","volume":"405","author":"Spilman","year":"2011","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116776_bib32","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1016\/j.jmb.2011.07.036","article-title":"The Staphylococcus aureus pathogenicity island 1 protein gp6 functions as an internal scaffold during capsid size determination","volume":"412","author":"Dearborn","year":"2011","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116776_bib33","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1111\/j.1365-2958.2009.06634.x","article-title":"Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations","volume":"72","author":"Ubeda","year":"2009","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib34","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.virol.2010.08.036","article-title":"The complete genomes of Staphylococcus aureus bacteriophages 80 and 80alpha--implications for the specificity of SaPI mobilization","volume":"407","author":"Christie","year":"2010","journal-title":"Virology"},{"key":"10.1016\/j.celrep.2025.116776_bib35","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1016\/j.ijmm.2016.08.005","article-title":"Identification and functional study of type III-A CRISPR-Cas systems in clinical isolates of Staphylococcus aureus","volume":"306","author":"Cao","year":"2016","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib36","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1038\/ismej.2016.163","article-title":"Phage-inducible islands in the Gram-positive cocci","volume":"11","author":"Martinez-Rubio","year":"2017","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2025.116776_bib37","first-page":"D535","article-title":"CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers","volume":"48","author":"Pourcel","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib38","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/nar\/gkad123","article-title":"Identification and characterization of thousands of bacteriophage satellites across bacteria","volume":"51","author":"de Sousa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib39","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1128\/AAC.01689-12","article-title":"Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals","volume":"57","author":"Kinnevey","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.celrep.2025.116776_bib40","doi-asserted-by":"crossref","first-page":"2426","DOI":"10.1128\/JB.187.7.2426-2438.2005","article-title":"Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain","volume":"187","author":"Gill","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.celrep.2025.116776_bib41","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1111\/j.1365-2958.2006.05441.x","article-title":"Prophages of Staphylococcus aureus Newman and their contribution to virulence","volume":"62","author":"Bae","year":"2006","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib42","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41586-023-06743-9","article-title":"Bacterial cGAS senses a viral RNA to initiate immunity","volume":"623","author":"Banh","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib43","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010146","article-title":"Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis","volume":"18","author":"Ibarra-Chavez","year":"2022","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116776_bib44","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005609","article-title":"Virus satellites drive viral evolution and ecology","volume":"11","author":"Frigols","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116776_bib45","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1098\/rspb.2001.1945","article-title":"Antagonistic coevolution between a bacterium and a bacteriophage","volume":"269","author":"Buckling","year":"2002","journal-title":"Proc. Biol. Sci."},{"key":"10.1016\/j.celrep.2025.116776_bib46","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1128\/jb.150.2.815-825.1982","article-title":"Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance","volume":"150","author":"Horinouchi","year":"1982","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.celrep.2025.116776_bib47","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature14245","article-title":"Cas9 specifies functional viral targets during CRISPR-Cas adaptation","volume":"519","author":"Heler","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib48","first-page":"3546","article-title":"A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration","volume":"49","author":"Jakhanwal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib49","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1038\/nsmb.2820","article-title":"Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity","volume":"21","author":"Nunez","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2025.116776_bib50","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/j.molcel.2022.01.012","article-title":"Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response","volume":"82","author":"Maguin","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib51","doi-asserted-by":"crossref","first-page":"4399","DOI":"10.1038\/ncomms5399","article-title":"Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages","volume":"5","author":"Hynes","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2025.116776_bib52","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.chom.2019.09.002","article-title":"Cas9 Cleavage of Viral Genomes Primes the Acquisition of New Immunological Memories","volume":"26","author":"Nussenzweig","year":"2019","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116776_bib53","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.plasmid.2013.12.001","article-title":"Sequence determinants for DNA packaging specificity in the S. aureus pathogenicity island SaPI1","volume":"71","author":"Bento","year":"2014","journal-title":"Plasmid"},{"key":"10.1016\/j.celrep.2025.116776_bib54","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nature17436","article-title":"The diversity-generating benefits of a prokaryotic adaptive immune system","volume":"532","author":"van Houte","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib55","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1128\/JB.01412-07","article-title":"Phage response to CRISPR-encoded resistance in Streptococcus thermophilus","volume":"190","author":"Deveau","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.celrep.2025.116776_bib56","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1093\/nar\/gkab1299","article-title":"Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system","volume":"50","author":"Aviram","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib57","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1093\/nar\/gkab1193","article-title":"Unique properties of spacer acquisition by the type III-A CRISPR-Cas system","volume":"50","author":"Zhang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib58","doi-asserted-by":"crossref","first-page":"9787","DOI":"10.1093\/nar\/gkaa685","article-title":"Spacer acquisition by Type III CRISPR-Cas system during bacteriophage infection of Thermus thermophilus","volume":"48","author":"Artamonova","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib59","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/nature13637","article-title":"Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting","volume":"514","author":"Goldberg","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib60","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/s41586-021-03206-x","article-title":"The Card1 nuclease provides defence during type III CRISPR immunity","volume":"590","author":"Rostol","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib61","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.chom.2017.07.016","article-title":"Broad Targeting Specificity during Bacterial Type III CRISPR-Cas Immunity Constrains Viral Escape","volume":"22","author":"Pyenson","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116776_bib62","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1056\/NEJM199808203390806","article-title":"Staphylococcus aureus infections","volume":"339","author":"Lowy","year":"1998","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.celrep.2025.116776_bib63","series-title":"Janeway\u2019s Immunobiology","first-page":"473","author":"Murphy","year":"2017"},{"key":"10.1016\/j.celrep.2025.116776_bib64","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/nature14237","article-title":"Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity","volume":"519","author":"Nunez","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib65","doi-asserted-by":"crossref","first-page":"5569","DOI":"10.1093\/nar\/gks216","article-title":"Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli","volume":"40","author":"Yosef","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2025.116776_bib66","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.chom.2021.11.014","article-title":"Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition","volume":"30","author":"Dimitriu","year":"2022","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2025.116776_bib67","first-page":"816","article-title":"A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids","volume":"337","author":"Boyd","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2025.116776_bib68","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","volume":"337","author":"Jinek","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.celrep.2025.116776_bib69","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/s41586-019-1257-5","article-title":"Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage","volume":"570","author":"Meeske","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib70","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nature11927","article-title":"A bacteriophage encodes its own CRISPR\/Cas adaptive response to evade host innate immunity","volume":"494","author":"Seed","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib71","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003844","article-title":"Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids","volume":"9","author":"Jiang","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2025.116776_bib72","doi-asserted-by":"crossref","first-page":"e00227-10","DOI":"10.1128\/mBio.00227-10","article-title":"Multidrug-resistant enterococci lack CRISPR-cas","volume":"1","author":"Palmer","year":"2010","journal-title":"mBio"},{"key":"10.1016\/j.celrep.2025.116776_bib73","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nrmicro2393","article-title":"The phage-related chromosomal islands of Gram-positive bacteria","volume":"8","author":"Novick","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib74","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2020.0464","article-title":"CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens","volume":"377","author":"Pursey","year":"2022","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.celrep.2025.116776_bib75","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/305709a0","article-title":"The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage","volume":"305","author":"Kreiswirth","year":"1983","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2025.116776_bib76","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/0092-8674(92)90101-H","article-title":"Sorting of protein A to the staphylococcal cell wall","volume":"70","author":"Schneewind","year":"1992","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2025.116776_bib77","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.virol.2012.05.026","article-title":"The roles of SaPI1 proteins gp7 (CpmA) and gp6 (CpmB) in capsid size determination and helper phage interference","volume":"432","author":"Damle","year":"2012","journal-title":"Virology"},{"key":"10.1016\/j.celrep.2025.116776_bib78","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.1318","article-title":"Enzymatic assembly of DNA molecules up to several hundred kilobases","volume":"6","author":"Gibson","year":"2009","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2025.116776_bib79","article-title":"Genetic manipulation of Staphylococcus aureus","volume":"32","author":"Schneewind","year":"2014","journal-title":"Curr. Protoc. Microbiol."},{"key":"10.1016\/j.celrep.2025.116776_bib80","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3390\/mps1030027","article-title":"A Rapid Bacteriophage DNA Extraction Method","volume":"1","author":"Jakociune","year":"2018","journal-title":"Methods Protoc."},{"key":"10.1016\/j.celrep.2025.116776_bib81","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"Galaxy","year":"2022","journal-title":"Nucleic Acids Res."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725015487?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124725015487?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:50:24Z","timestamp":1791262224000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124725015487"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":81,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S2211124725015487"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116776","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Phage induction of Staphylococcus aureus pathogenicity islands promotes the CRISPR-Cas adaptive immune response","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2025.116776","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116776"}}